Objective To make a comparison of the application value of c-TCD and c-TTE in the diagnosis of migraine with right to left shunt（ RLS） in heart. Methods A total of 110 cases of patients with migraine cured in Neurology Department of Hu'nan Brain Hospital from June 2017 to December 2017 were selected. The positive rates of RLS in these selected patients were examined by c-TTE and c-TCD respectively， with transesophageal contrast echocardiography（ CTEE） as the gold standard. The differences of positive rate of RLS in the two examinations were studied. According to the amount of microbubbles， the c-TCD was divided into 3 levels. The difference of the positive rate of c-TTE in different level of microbubbles were compared. At the same time， the correlation study was carried out between the diameter of Patent Foramen Ovale（ PFO） and the amount of microbubbles. Results RLS detection was higher under c-TCD than that under c-TTE（ 75.45% vs 57.27%， χ2=8.092， P=0.004）. The differences had statistical significance. The c-TTE compared with c-TEE showed： sensitivity 69.66%， specificity 100%， and accuracy 75.40%. The detection of c-TCD in small amounts of microbubbles was significantly higher than that of c-TTE（ χ2=4.082， P=0.043；χ2=4.271，P=0.039）. After Pearson correlation analysis， a moderately positive correlation was presented between the diameter of PFO and the amount of microbubbles（ r=0.525） in 62 patients with positive c-TTE examination. Conclusions The amount of microbubbles increases with the diameter of PFO. C-TCD can be used as the preferred method of screening for migraine patients with or without RLS.